[R-sig-eco] Quantifying functional trait diversity through Gower distance and pcoa

Phil Novack-Gottshall pnovack-gottshall at ben.edu
Tue Nov 16 16:24:03 CET 2010

Dear Chris,

You might consider the FD library, which allows measurement of a range 
of functional diversity metrics, and includes functions for Gower 
distance (and, within other functions, PCoA, using, I believe, the 
dudi.pco function from the ade4 library).  A benefit of the library's 
functions is control over the number of dimensions to include.

Laliberté, E., and B. Shipley. 2010. FD: Measuring functional diversity 
(FD) from multiple traits, and other tools for functional ecology, 
Version 1.0-9.


On 11/16/2010 9:08 AM, chris mcowen wrote:
> Dear List,
> I am relatively new to this area of ecology and R, coming from a
> phylogenetic background. I am looking to quantify functional trait
> diversity in in order to plot global functional trait diversity
> hotspots. My trait data are categorical and all indicies of functional
> diversity require continuous data.
> My approach was to generate a distance matrix based on the Gower
> method - i have done this with vegdist- and then i was planning on
> running a pcoa on these to generate the continuous data to use in the
> calculation of functional diversity indicies.
> I have two questions:-
> First, does this make sense, i appreciate i will loose information this way.
> Second, I have looked at vegan but can not see a way to run a pcoa on
> the output from a vegdist analysis, is this possible and once again
> does this make sense?
> Any help would be greatly appreciated,
> Chris
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  Phil Novack-Gottshall
  Assistant Professor
  Department of Biology
  Benedictine University
  5700 College Road
  Lisle, IL 60532

  pnovack-gottshall at ben.edu
  Phone: 630-829-6514
  Fax: 630-829-6547
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